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Ccp4 Newsletter on Protein Crystallography CCP4 NEWSLETTER ON PROTEIN CRYSTALLOGRAPHY An informal Newsletter associated with the BBSRC Collaborative Computational Project No. 4 on Protein Crystallography. Number 42 Summer 2005 Contents News 1. CCP4 General news html Peter Briggs(1), Charles Ballard(1), Martyn Winn(1), Norman Stein(1), Daniel Rolfe(1), Francois Remacle(1), Graeme Winter(1), Ronan Keegan(1), Paul Emsley(2) 1CCP4, Daresbury Laboratory, Warrington WA4 4AD, UK, 2Structural Biology department, York University, York, UK 2. Developments in CCP4i html Peter Briggs, Charles Ballard, Martyn Winn, Francois Remacle CCP4, Daresbury Laboratory, Warrington WA4 4AD, UK 3. Report on the CCP4 Workshop at ACA 2005, Orlando, Florida html Peter Briggs CCP4, Daresbury Laboratory, Warrington WA4 4AD, UK 4. Diamond: Status Report on MX Beamlines and Computing pdf doc Alun Ashton, Katherine McAuley, Sara Fletcher, Jose Brandao-Neto, Liz Duke, Gwyndaf Evans, Ralf Flaig, Bill Pulford, Thomas Sorensen, Richard Woolliscroft Diamond Light Source, Diamond House, Chilton, OX11 0DE Software 5. Crank, Crunch2 and Bp3: A platform for rapid automated structure determination html Steven R. Ness, Irakli Sikharulidze, R.A.G de Graaff, Navraj S. Pannu Biophysical Structural Chemistry, Leiden Institute of Chemistry, P.O. Box 9502, 2300 RA Leiden, The Netherlands 6. CHOOCH – automatic analysis of fluorescence scans and determination of optimal X-ray wavelengths for MAD and SAD doc Gwyndaf Evans Diamond Light Source, Diamond House, Chilton, OX11 0DE 7. Coot news pdf Paul Emsley(1), Kevin Cowtan(1), Bernhard Lohkamp(2) 1Structural Biology department, York University, York, UK, 2Department of Medical biochemistry and biophysics, Karolinska institutet, Stockholm, Sweden 8. The Phenix refinement framework doc Afonine P.V., Grosse-Kunstleve R.W, Adams P.D. Lawrence Berkeley National Laboratory, One Cyclotron Road, BLDG 64R0121, Berkeley, CA 94720 USA Methodology 9. On the Fourier series truncation peaks at subatomic resolution doc Anne Bochow, Alexandre Urzhumtsev Physics Department, Faculty of Sciences and Technologies, University H. Poincaré Nancy 1, B.P. 239, 54506 Vandoeuvre-lès-Nancy, France 10. Characterization of X-ray data sets doc Peter H. Zwart, Ralf W. Grosse-Kunsteleve, Paul D. Adams Lawrence Berkeley National Laboratory, 1 Cyclotron Road, BLDG 64R0121, Berkeley California 94720-8118, USA Editor: Francois Remacle Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, UK NOTE: The CCP4 Newsletter is not a Contributions are invited for the next issue of the newsletter, and formal publication and permission to refer to should be sent to Francois Remacle by e-mail at or quote from the articles reproduced here mailto:[email protected]. HTML is preferred but other editable must be referred to the authors. formats are also acceptable. CCP4 Main Page CCP4 General news: Peter Briggs, Charles Ballard, Martyn Winn, Daniel Rolfe, Graeme Winter, Ronan Keegan, Norman Stein, Francois Remacle, Paul Emsley* CCP4, Daresbury Laboratory, Warrington WA4 4AD, UK *Structural Biology department, York University, York,UK Table of Content · Future Release 6.0 of CCP4 · CCP4 and BIOXHIT · CCP4 and e-HTPX · CCP4 automations projects · AutoAmore · HAPPy Future Release 6.0 of CCP4 General information The Collaborative Computational Project Number 4 in Protein Crystallography was set up in 1979 to support collaboration between researchers working on such software in the UK, and to assemble a comprehensive collection of software to satisfy the computational requirements of the relevant UK groups. CCP4 was originally supported by the UK Science and Engineering Research Council (SERC), and is now supported by the Biotechnology and Biological Sciences Research Council (BBSRC). The project is coordinated at CCLRC Daresbury Laboratory. The results of this effort gave rise to the CCP4 program suite, which is now distributed to academic and commercial users world-wide. During its history it passed through different releases. Each of these releases adding new programs from the developers community, offering new tools and techniques to make the suite more complete in order to provide a powerful tool to its users. Now, version 6.0 is being developed and tested. We are going to outline below its new features and improvements from last release. What's new In future releases, the CCP4 Suite will be separated into a number of packages, in order to provide the user with an easier way to download and install the programs, and in order to facilitate subsequent updates. In release 6.0, the following different packages will be available: CCP4 program suite: Containing usual programs, libraries, tutorials, examples, CCP4i and new tools as you will see below. CCP4 Molecular Graphics: From authors Liz Potterton and Stuart McNicholas, CCP4MG enables to displays molecules with simple, flexible selection tools and a variety of display styles and colouring schemes through a simple interface. It also provides different structure analysis. COOT: From author Paul Emsley, Coot is a tool that enables to display maps and models and allows certain model manipulations: idealization, real space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers, Ramachandran plots, model validation and others... Phaser 1.3 and CCTBX: Developed at university of Cambridge, Phaser is a program for phasing macromolecular crystal structures with maximum likelihood methods. It currently has methods for brute force and fast likelihood- based rotation and translation functions for molecular replacement. Methods for experimental phasing are under development. The Computational Crystallography Toolbox (cctbx) is being developed as the open source component of the PHENIX system. It contains different modules for different purpose in macromolecular crystallography. CHOOCH: From author Gwyndaf Evans, The program CHOOCH determines values of anomalous scattering factors from raw fluorescence spectra. The basic CCP4 program suite package will provide a series of new tools: Bp3*: From author Navraj Pannu, Bp3 is a program for obtaining phase information from an S/MIR(AS) and/or S/MAD experiment(s) by multivariate likelihood estimation. Bp3 takes part in the works done by crank. Crank*: From author Steven Ness, Crank is a new suite of programs for automated macromolecular structure solution. It uses an XML based framework to join many different crystallography programs into a unified whole. CRANK is intimately linked to the CCP4 package, using CCP4i for job setup and control. Superpose and SSM: From author Eugine Krissinel, (SSM) Secondary Structure Matching is a tool for protein structure comparison in 3D. Superpose is a program making secondary structure superposition using the functions provided by SSM library. Pirate: From author Kevin Cowtan, Pirate is a program performing statistical phase improvement by classifying the electron density map by sparseness/denseness and order/disorder, with the aim of obtaining superior results to conventional solvent mask based methods without requiring knowledge of the solvent content. Clipper Utilities: From author Kevin Cowtan, these are some utilities providing useful functionnalities from Clipper libraries. Chainsaw: From author Norman Stein, Chainsaw is a utility for Molecular Replacement, which mutates a template pdb file using a sequence alignment between the target and template. * For more information about the work done by crank and Bp3 you can read the article concerning them in this newletter. Updates from version 5 of CCP4 In addition to the new series of programs and packages, CCP4 program suite will also include the up to date version of the CCIF, Clipper, MMDB and CCP4 Libraries, the latest versions of Pdb-Extract, Molrep, Mosflm, Refmac, Sfcheck and Scala and the updated version of CCP4i (you can read the article concerning the new version of CCP4i). OnGoing Projects and Pre-releases In addition to CCP4 v6.0 there are other projects that are ongoing around CCP4, new delivery systems, new programs. Some of these will available as pre-release together with release of CCP4. Currently there are the following items that will be pre-released: Linux Install Wizard: Based on the installshield technology this project is trying to create an installer as straightforward and robust as its bigger brother available on windows. Pointless: From author Phil Evans, Pointless is a program that enables to determine the Laue groups using the symmetry functionalities of CCTBX. CCP4 and BIOXHIT BIOXHIT started in January 2004 and is an "integrated project" funded for four years within the 6th Framework Programme of the European Commission. BIOXHIT is coordinating scientists at all European synchrotrons and leading software developers in a joint effort to develop, assemble and provide a highly effective technology platform for Structural Genomics. CCP4 is involved in workpackages which aim to implement data management and project tracking in structure solution, and in work which complements the CCP4 Automation Project. The project currently funds one-full time programmer. As a key part of this work the CCP4i database is currently being expanded and standardised as a Project database for non-CCP4(i) applications operating in a multi- user computing environment. The scope of the data stored in the database - both the raw data and the history record information - will also be extended as part of the project, and visualisation tools will be developed to help users make sense of the data. The aim is
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